prevent applauncher and treeannotator to grab focus when running from CLI. fixex #1212

Author: rbouckaert

release/Linux/jrebin/applauncher

@@ -50,10 +50,16 @@ else
     export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":/usr/local/lib
 fi
 
+if [ "$#" -gt 1 ]; then
+    HEADLESS="-Djava.awt.headless=true"
+else
+    HEADLESS=""
+fi
+
 # use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations 
 # this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
 if [ -n "$BEAST_EXTRA_LIBS" ]; then 
-  "$JAVA" -Dlauncher.wait.for.exit=true -Xss256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher $*
+  "$JAVA" $HEADLESS -Dlauncher.wait.for.exit=true -Xss256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher $*
 else	
-  "$JAVA" -Dlauncher.wait.for.exit=true -Xss256m -Xmx8g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher $*
+  "$JAVA" $HEADLESS -Dlauncher.wait.for.exit=true -Xss256m -Xmx8g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher $*
 fi

release/Linux/jrebin/treeannotator

@@ -30,5 +30,12 @@ if [ -z "$JAVA_HOME" ]; then
 else
   JAVA="$JAVA_HOME"/bin/java
 fi
-"$JAVA" -Dlauncher.wait.for.exit=true -Xss256m -Xmx8g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.TreeAnnotatorLauncher $*
+
+if [ "$#" -gt 1 ]; then
+    HEADLESS="-Djava.awt.headless=true"
+else
+    HEADLESS=""
+fi
+
+"$JAVA" $HEADLESS -Dlauncher.wait.for.exit=true -Xss256m -Xmx8g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.TreeAnnotatorLauncher $*